Hi Klaus,
Actually, I need to apologize to the community. I was wrong — the midpoint()
function works perfectly as is!
I had built a little example with dummy data that was confusing me. But, I
changed my example and now I understand what’s going on. After running the
midpoint() function, it
Hi,
I’m writing with an issue using the chronos function in ape:
I have a rooted supertree of 186 taxa (genetic & linguistic data), and am
trying to time-calibrate with a set of divergence dates (genetic & linguistic;
available for about 1/3 of nodes).
I’m using chronos and calling agemin
Hi Knud,
in phangorn I try to take care that the node labels are assigned to the
right nodes after using midpoint, see attached code and pic. It seems to
work quite nicely. It would be useful if you could supply a reproducible
example or the tree you have problems with and open otherwise an issue
Hi Jarrod,
Thanks very much for your fast reply. Egg-laying and live-bearing are
dispersed throughout the tree ( I have attached a PDF of a traitplot with
egg-laying and live-bearing on it; blue is egg-laying and red is
live-bearing), being universal in chimaeras and skates, and found in
several
Hi Ting-Wen,
as Ted pointed out, if and how one has to correct for multiple tests
is a huge topic. Perhaps looking at the literature and making your own
opinion on this matter would be the best choice (for example, Perneger
1998 - British Medical Journal and Garcia 2004 - Oikos, present two
Hi All,
I am trying to look at the correlated evolution of traits using the
threshold model as implemented in phytools::threshBayes (Revell 2014) and
MCMCglmmRAM (Hadfield 2015). My understanding from Hadfield 2015 is that
the reduced animal models should yeild equivalent results, yet having run
Hi Chris,
I think MCMCglmm is probably giving you the right answer. There are huge
chunks of the phylogeny that are either egg-laying and live-bearing. The
non-phylogenetic model shows a strong relationship between reproductive
mode and depth, and that might be causal or it might just be
Hi Chris,
OK - stick with the RAM model, the h2 is so high you will run into
numerical issues otherwise. In the two-trait model you might want to add
in us(at.level(trait,1)):units into the random effects (make sure it is
not the last term in the random formula) in case log.dep has a h2
Hi Chris,
I think ngen in threshbayes is not the number of full iterations (i.e. a
full update of all parameters), but the number of full iterations
multiplied by the number of nodes (2n-1). With n=600 species this means
threshbayes has only really done about 8,000 iterations (i.e. about
Hi Jarrod,
I hadn't appreciated that the clustering of reproductive modes on the tree
might limit out ability to detect some of these relationships. This is in
fact a step in testing reproduction as an ordinal variable (egg-laying,
lecithotrophic live-bearing, and matrotrophic live-bearing) which
It seems that .compressTipLabel's running times are proportional to N
(number of trees) and to log(n) (n: nb of tips).
R> tr <- rmtree(1e4, 1e4) # takes ~5 minutes
R> system.time(a <- .compressTipLabel(tr))
utilisateur système écoulé
20.904 0.376 21.275
R>
Hi,
Is there any way to use the updated root() function in ape ver 4.0 to find and
set the midpoint root in a tree? I greatly appreciate the updated root()
function to include the “edgelabel = TRUE” option, so that when I have
bootstrapping support values listed as node labels, they get
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